Fig 1.
The circular representation of the complete mitochondrial genome of T. palmi.
Direction of gene transcription is indicated by arrows in entire complete genome. PCGs are shown as purple arrows, rRNA genes as pink arrows, tRNA genes as peach color arrows and CR regions as gray rectangles. The GC content is plotted using a black sliding window, as the deviation from the average GC content of the entire sequence. The GC-skew is plotted using a colored sliding window (green and orchid color), as the deviation from the average GC skew of the entire sequence. The figure was drawn using the CGView online server (http://stothard.afns.ualberta.ca/cgview_server/) with default parameters. The species photograph was taken by the second author (KT) using Leica Microscope DM1000 with Leica software application suite (LAS EZ) and edited manually in Adobe Photoshop CS 8.0.
Table 1.
List of annotated mitochondrial genes of T. palmi and its characteristic features.
The PCGs and rRNA genes are represented by standard nomenclature, tRNAs are represented as trn followed by the IUPAC-IUB single letter amino acid codes. (+) values in strand represent as heavy (H) and (-) values represent as light (L). IGN represents (+) values as intergenic nucleotides and (-) values as overlapping regions. CR represents the control region.
Table 2.
Nucleotide composition and skewness in different Thysanoptera mt genomes considered for comparative analysis.
Fig 2.
(A) Ratio estimation, box plot for pairwise divergence of Ka/Ks ratio for each one of the mitochondrial PCGs. (B) Evolutionary rates (Ka/Ks) of individuals PCGs of T. palmi with other thrips species.
Fig 3.
Predicted structural elements for control regions (CRs) of T. palmi.
Fig 4.
Linearized view of complete mitochondrial genome organization and gene rearrangement, transposition, inversion, and inverse transposition in T. palmi compared with the ancestral type of the insect (A. bakeri).
The gray color blocks show the conserve gene blocks of T. palmi and A. bakeri. The green color blocks show the conserve gene blocks of T. palmi and other Thysanoptera species. The pink color block shows the extra tRNA present in T. imaginis. Gene blocks with underline shows the position of genes in minority strand (red for PCGs, green for rRNAs, and blue for tRNAs). Different shapes of arrows are used for showing transposition, inversion, and inverse transposition. Gene nomenclature: atp6 and atp8; ATP synthase subunits 6 and 8; cytb: cytochrome b; cox1–3: cytochrome c oxidase subunits 1–3; nad1–6 and nad4L: NADH dehydrogenase subunits 1–6 and 4L; rrnS and rrnL: small and large subunit ribosomal RNA (rRNA) genes; Transfer RNA genes are denoted by a one-letter symbol according to the IPUCIUB single-letter amino acid codes. CR indicates the control region.
Fig 5.
Bayesian phylogenetic tree inferred by 13 PCGs of thrips mt genomes.
The Bayesian posterior probabilities and Maximum likelihood bootstrap supports are superimposed with each node. The tree is drawn to scale with values indicated along with the branches (BI/ML).